jean — Molecular Biology & Genomics

match_part_by_sequence

Read-only

Identify a stretch of DNA by asking the iGEM Registry which published part carries exactly those bases, and hand back that part's own description, Sequence-Ontology role, literature citation and license. The match is decided by comparing bases, never by a name — so a pipeline can label a fragment it has assembled, or check that a feature really is the part it is called.

Input Schema

TableJSON Schema

Name	Required	Description
`cap`	No	most candidate sequences to fetch and compare before stopping and saying so.
`name`	No	a name to narrow the candidates by (a feature name, or a part id like BBa_R0040). It only narrows: the bases decide the match. Leave it empty to compare every candidate of this exact length, which is slower and can be far more requests.
`_files`	No	The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
`_subject`	No	The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
`sequence`	Yes	the bases to identify — a feature’s span, an assembled fragment, a pasted oligo.

Output Schema

TableJSON Schema

Name	Required	Description
`page`	Yes	the registry page, so the claim can be checked without us
`part`	Yes	the best match’s registry id, exact before reverse-complement
`role`	Yes	its Sequence-Ontology role, as the registry files it
`title`	Yes	the registry’s own short title for that part
`strand`	Yes	`exact` when the bases agree as given, `reverse-complement` when they agree flipped
`licence`	Yes	the SPDX identifier the registry states for that part
`matched`	Yes	whether any compared part carries these exact bases
`matches`	Yes	every part that carries these bases — several may, and the registry keeps them apart
`coverage`	Yes	what was and was not compared: the population at this length, the candidates the narrowing produced, how many were read back, and whether the cap stopped it. A null answer is only as strong as this.
`description`	Yes	the registry’s own prose — the half a coordinate cannot tell you

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A4.3/5.0

Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare read-only, open-world, and non-destructive behavior. The description adds that it queries the remote iGEM Registry, compares actual bases rather than names, and returns part description, Sequence-Ontology role, citation, and license; it does not discuss rate limits or cap behavior, which the schema covers.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two sentences, front-loaded with the core purpose and followed by clear use cases. Every clause earns its place and there is no redundant wording.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

The tool has an output schema and annotations that cover safety and external interaction, and the input schema fully documents all parameters. The description supplies the purpose, matching logic, and returned fields, so an agent has enough context to invoke it correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so all five parameters are documented in the schema, including name's narrowing role and cap's limit. The description reinforces that bases decide the match, but this is already stated in the schema, and cap is not mentioned at all, so the description adds little parameter-level meaning beyond the baseline.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description gives a specific verb and resource: identify a DNA stretch by asking the iGEM Registry which published part carries exactly those bases. It also explicitly distinguishes sequence-based identification from name-based lookup, so an agent can tell it apart from sibling tools like lookup_gene or search_records.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

It names two concrete scenarios: labeling an assembled fragment or verifying that a feature is the part it is called. It does not name alternative tools or state when not to use this tool, so it provides clear context but no explicit exclusions.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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